ABSTRACT
Nucleases play pivotal roles in DNA repair and apoptosis. Moreover, they have various applications in biotechnology and industry. Among nucleases, TatD has been characterized as an exonuclease with various biological functions in different organisms. Here, we biochemically characterized the potential TatD nuclease from Thermus thermophilus. The tatD gene from T. thermophilus was cloned, then the recombinant TatD nuclease was expressed and purified. Our results revealed that the TthTatD nuclease could degrade both single-stranded and double-stranded DNA, and its activity is dependent on the divalent metal ions Mg2+ and Mn2+. Remarkably, the activity of TthTatD nuclease is highest at 37 °C and decreases with increasing temperature. TthTatD is not a thermostable enzyme, even though it is from a thermophilic bacterium. Based on the sequence similarity and molecular docking of the DNA substrate into the modeled TthTatD structure, several key conserved residues were identified and their roles were confirmed by analyzing the enzymatic activities of the site-directed mutants. The residues E86 and H149 play key roles in binding metal ions, residues R124/K126 and K211/R212 had a critical role in binding DNA substrate. Our results confirm the enzymatic properties of TthTatD and provide a primary basis for its possible application in biotechnology.
ABSTRACT
Background: Evidence suggests that type 2 diabetes (T2D) is an independent risk factor for Alzheimer's disease (AD), sharing similar pathophysiological traits like impaired insulin signaling. Objective: To test the association between plasma insulin and cerebrospinal fluid (CSF) AD pathology. Methods: A total of 304 participants were included in the Alzheimer's Disease Neuroimaging Initiative, assessing plasma insulin and CSF AD pathology. We explored the cross-sectional and longitudinal associations between plasma insulin and AD pathology and compared their associations across different AD clinical and pathological stages. Results: In the non-demented group, amyloid-ß (Aß)+ participants (e.g., as reflected by CSF Aß42) exhibited significantly lower plasma insulin levels compared to non-demented Aß-participants (pâ<â0.001). This reduction in plasma insulin was more evident in the A+T+ group (as shown by CSF Aß42 and pTau181 levels) when compared to the A-T- group within the non-dementia group (pâ=â0.002). Additionally, higher plasma insulin levels were consistently associated with more normal CSF Aß42 levels (pâ<â0.001) across all participants. This association was particularly significant in the Aß-group (pâ=â0.002) and among non-demented individuals (pâ<â0.001). Notably, baseline plasma insulin was significantly correlated with longitudinal changes in CSF Aß42 (pâ=â0.006), whereas baseline CSF Aß42 did not show a similar correlation with changes in plasma insulin over time. Conclusions: These findings suggest an association between plasma insulin and early Aß pathology in the early stages of AD, indicating that plasma insulin may be a potential predictor of changes in early Aß pathology.
Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Insulin , Peptide Fragments , tau Proteins , Humans , Alzheimer Disease/blood , Alzheimer Disease/pathology , Male , Female , Amyloid beta-Peptides/blood , Amyloid beta-Peptides/cerebrospinal fluid , Insulin/blood , Aged , Cross-Sectional Studies , Peptide Fragments/blood , Peptide Fragments/cerebrospinal fluid , tau Proteins/blood , tau Proteins/cerebrospinal fluid , Longitudinal Studies , Biomarkers/blood , Biomarkers/cerebrospinal fluid , Aged, 80 and over , Middle AgedABSTRACT
Depression and Alzheimer's disease (AD) are prevalent neuropsychiatric disorders with intriguing epidemiological overlaps. Their interrelation has recently garnered widespread attention. Empirical evidence indicates that depressive disorders significantly contribute to AD risk, and approximately a quarter of AD patients have comorbid major depressive disorder, which underscores the bidirectional link between AD and depression. A growing body of evidence substantiates pervasive sex differences in both AD and depression: both conditions exhibit a higher incidence among women than among men. However, the available literature on this topic is somewhat fragmented, with no comprehensive review that delineates sex disparities in the depression-AD correlation. In this review, we bridge these gaps by summarizing recent progress in understanding sex-based differences in mechanisms, genetics, and therapeutic prospects for depression and AD. Additionally, we outline key challenges in the field, holding potential for improving treatment precision and efficacy tailored to male and female patients' distinct needs.
ABSTRACT
As a vital factor in technological innovation, patentee plays a significant role in the process of scientific and technological innovation, researching patentee has attracted the attention of experts and scholars. Previously, scholars have mainly quantified patent indicators or constructed homogeneous information networks to analyze patentees, but these methods cannot objectively measure the impact of patentees. Therefore, this study proposes a novel approach to assessing patentee impact based on a heterogeneous information network. The proposed method distinguishes the weight of different types of nodes using a weighted mechanism and extracts three types of fine-grained characteristics of network nodes. This approach results in the construction of a heterogeneous patent innovation network and the development of a new patentee impact assessment algorithm called CWAPN. Using Chinese green patents in the field of energy conservation and environmental protection as an example, experimental results show that the CWAPN algorithm can effectively assess the impact of patentees. Thereby identifying patentees who have made outstanding contributions to sustainable development in China.
ABSTRACT
Bacterial RecJ exhibits 5'â3' exonuclease activity that is specific to ssDNA; however, archaeal RecJs show 5' or 3' exonuclease activity. The hyperthermophilic archaea Methanocaldococcus jannaschii encodes the 5'-exonuclease MjRecJ1 and the 3'-exonuclease MjRecJ2. In addition to nuclease activity, archaeal RecJ interacts with GINS, a structural subcomplex of the replicative DNA helicase complex. However, MjRecJ1 and MjRecJ2 do not interact with MjGINS. Here, we report the structural basis for the inability of the MjRecJ2 homologous dimer to interact with MjGINS and its efficient 3' hydrolysis polarity for short dinucleotides. Based on the crystal structure of MjRecJ2, we propose that the interaction surface of the MjRecJ2 dimer overlaps the potential interaction surface for MjGINS and blocks the formation of the MjRecJ2-GINS complex. Exposing the interaction surface of the MjRecJ2 dimer restores its interaction with MjGINS. The cocrystal structures of MjRecJ2 with substrate dideoxynucleotides or product dCMP/CMP show that MjRecJ2 has a short substrate binding patch, which is perpendicular to the longer patch of bacterial RecJ. Our results provide new insights into the function and diversification of archaeal RecJ/Cdc45 proteins.
Subject(s)
Archaeal Proteins , Archaeal Proteins/chemistry , Archaeal Proteins/metabolism , Archaeal Proteins/genetics , Crystallography, X-Ray , Methanocaldococcus/enzymology , Methanocaldococcus/metabolism , Protein Binding , Protein Multimerization , DNA Helicases/metabolism , DNA Helicases/chemistry , DNA Helicases/genetics , Models, Molecular , Exodeoxyribonucleases/metabolism , Exodeoxyribonucleases/chemistry , Exodeoxyribonucleases/geneticsABSTRACT
Understanding the link between microbial community stability and assembly processes is crucial in microbial ecology. Here, we investigated whether the impact of biotic disturbances would depend on the processes controlling community assembly. For that, we performed an experiment using soil microcosms in which microbial communities assembled through different processes were invaded by Escherichia coli. We show that the ecological assembly process of the resident community plays a significant role in invader-resident competition, invader survival, and compositional stability of the resident community. Specifically, the resident communities primarily assembled through stochastic processes were more susceptible to invader survival. Besides, E. coli invasion acts as a biotic selection pressure, leading to competition between the invader and resident taxa, suppressing the stochasticity in the resident community. Taken together, this study provides empirical evidence for the interpretation of microbial community assemblage on their (potential) ecosystem functions and services, such as the prevention of pathogen establishment and the pathogenic states of soil microbiomes.
Subject(s)
Escherichia coli , Microbiota , Soil Microbiology , Escherichia coli/genetics , Ecosystem , Microbial Interactions , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purificationABSTRACT
BACKGROUND: Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional, functional, and metabolic) of the invasive and coalescent communities. RESULTS: Our results showed that coalescences significantly triggered changes in the resident community's succession trajectory and functionality (carbohydrate metabolism), even when the size of the invasive community is small (~ 5% of the resident density) and 99% of the invaders failed to survive. The invasion impact was mainly due to the high suppression of constant residents (65% on average), leading to a lose-lose situation where both invaders and residents suffered with coalescence. Our results showed that surviving residents could benefit from the coalescence, which supports the theory of "competition-driven niche segregation" at the microbial community level. Furthermore, the result showed that both short- and long-term coalescence effects were predicted by similarity and unevenness indexes of compositional, functional, and metabolic traits of invasive communities. This indicates the power of multi-level traits in monitoring microbial community succession. In contrast, the varied importance of different levels of traits suggests that competitive processes depend on the composition of the invasive community. CONCLUSIONS: Our results shed light on the process and consequence of community coalescences and highlight that resource competition between invaders and residents plays a critical role in soil microbial community coalescences. These findings provide valuable insights for understanding and predicting soil microbial community succession in frequently disturbed natural and agroecosystems. Video Abstract.
Subject(s)
Microbiota , Soil , Soil Microbiology , Bacteria/genetics , Bacteria/metabolismABSTRACT
Background: Silibinin has been found to inhibit glioblastoma (GBM) progression. However, the underlying molecular mechanism by which Silibinin regulates GBM process remains unclear. Methods: GBM cell proliferation, apoptosis, invasion, and stemness are assessed by cell counting kit-8 assay, EdU assay, flow cytometry, transwell assay, and sphere formation assay. Western blot is used to measure the protein expression levels of apoptosis-related markers, solute carrier family 1 member 5 (SLC1A5), and Yin Yang-1 (YY1). Glutamine consumption, glutamate production, and α-ketoglutarate production are detected to evaluate glutamine metabolism in cells. Also, SLC1A5 and YY1 mRNA levels are examined using quantitative real-time PCR. Chromatin immunoprecipitation assay and dual-luciferase reporter assay are used to detect the interaction between YY1 and SLC1A5. Mice xenograft models are constructed to explore Silibinin roles in vivo. Results: Silibinin inhibits GBM cell proliferation, invasion, stemness, and glutamine metabolism, while promotes apoptosis. SLC1A5 is upregulated in GBM and its expression is decreased by Silibinin. SLC1A5 overexpression abolishes the anti-tumor effect of Silibinin in GBM cells. Transcription factor YY1 binds to SLC1A5 promoter region to induce SLC1A5 expression, and the inhibition effect of YY1 knockdown on GBM cell growth, invasion, stemness, and glutamine metabolism can be reversed by SLC1A5 overexpression. In addition, Silibinin reduces GBM tumor growth by regulating YY1/SLC1A5 pathway. Conclusion: Silibinin plays an anti-tumor role in GBM process, which may be achieved via inhibiting YY1/SLC1A5 pathway.
ABSTRACT
Microbial biodegradation serves as an effective approach to treat oil pollution. However, the application of such methods for the degrading long-chain alkanes still encounters significant challenges. Comparative proteomics has extensively studied the intracellular proteins of bacteria that degrade short- and medium-chain alkanes, but the role and mechanism of extracellular proteins in many microorganism remain unclear. To enhance our understanding of the roles of extracellular proteins in the adaptation to long-chain alkanes, a label-free LC-MS/MS strategy was applied for the relative quantification of extracellular proteins of Pseudomonas aeruginosa SJTD-1-M (ProteomeXchange identifier PXD014638). 444 alkane-sentitive proteins were acquired and their cell localization analysis was performed using the Pseudomonas Genome Database. Among them, 111 proteins were found to be located in extracellular or Outer Membrane Vesicles (OMVs). The alkane-induced abundance of 11 extracellular or OMV target proteins was confirmed by parallel reaction monitoring (PRM). Furthermore, we observed that the expression levels of three proteins (Pra, PA2815, and FliC) were associated with the carbon chain length of the added alkane in the culture medium. The roles of these proteins in cell mobility, alkane emulsification, assimilation, and degradation were further discussed. OMVs were found to contain a number of enzymes involved in alkane metabolism, fatty acid beta-oxidation, and the TCA cycle, suggesting their potential as sites for facilitated alkane degradation. In this sense, this exoproteome analysis contributes to a better understanding of the role of extracellular proteins in the hydrocarbon treatment process.
Subject(s)
Pseudomonas Infections , Pseudomonas aeruginosa , Humans , Pseudomonas aeruginosa/genetics , Alkanes , Chromatography, Liquid , Tandem Mass Spectrometry , PseudomonasABSTRACT
Cyclic di-adenosine monophosphate (c-di-AMP) is a newly identified prokaryotic cyclic dinucleotide second messenger well elucidated in bacteria, while less studied in archaea. Here, we describe the enzymes involved in c-di-AMP metabolism in the hyperthermophilic archaeon Pyrococcus yayanosii. Our results demonstrate that c-di-AMP is synthesized from two molecules of ATP by diadenylate cyclase (DAC) and degraded into pApA and then to AMP by a DHH family phosphodiesterase (PDE). DAC can be activated by a wider variety of ions, using two conserved residues, D188 and E244, to coordinate divalent metal ions, which is different from bacterial CdaA and DisA. PDE possesses a broad substrate spectrum like bacterial DHH family PDEs but shows a stricter base selection between A and G in cyclic dinucleotides hydrolysis. PDE shows differences in substrate binding patches from bacterial counterparts. C-di-AMP was confirmed to exist in Thermococcus kodakarensis cells, and the deletion of the dac or pde gene supports that the synthesis and degradation of c-di-AMP are catalyzed by DAC and PDE, respectively. Our results provide a further understanding of the metabolism of c-di-AMP in archaea.
Subject(s)
Archaea , Bacterial Proteins , Archaea/metabolism , Bacterial Proteins/chemistry , Bacteria/metabolism , Phosphoric Diester Hydrolases/chemistry , Phosphoric Diester Hydrolases/genetics , Phosphoric Diester Hydrolases/metabolism , IonsABSTRACT
PURPOSE: This study aimed to investigate the cost-effectiveness of stent retriever (SR) versus best medical management (BMM) in patients with basilar artery occlusion (BAO) in China. METHODS: We used a two-step approach to compare the cost-effectiveness of SR plus BMM with that of BMM alone over 20 years. A decision tree was initially constructed for the first 3 months, followed by a Markov model for the subsequent period. Collected data on clinical aspects were extracted from the BAOCHE investigation, while costs-related information was sourced from previously published research. The key metric for evaluating the primary outcome was the incremental cost-effectiveness ratio (ICER), achieved $/QALY. The threshold for identifying SR as highly cost-effective was set at an ICER below $12,551/QALY, SR was deemed cost-effective if the ICER ranged from $12,551 to $37,654 per QALY. Uncertainty was addressed using scenario, one-way sensitivity, and probabilistic sensitivity analyses (PSA). FINDINGS: For Chinese patients with BAO, the 20-year cost per patient was $8678 with BMM alone and $21,988 for SR plus BMM. Effectiveness was 1.45 QALY for BMM alone, and 2.77 QALY for SR plus BMM. The ICER of SR + BMM versus BMM alone was $10,050 per QALY. The scenario and one-way sensitivity analyses revealed that in certain situations the ICER could exceed $12,551 per QALY, but remain below $37,654 per QALY. Results from the PSA suggested that SR was likely to be cost-effective for Chinese patients with BAO, with a probability exceeding 98% when considering a willingness-to-pay (WTP) threshold of $12,551 per QALY. IMPLICATIONS: Our study indicates that SR is an intervention option that is highly likely to be cost-effective for Chinese patients with BAO, with a probability of over 98% under the current WTP threshold of $12,551 per QALY.
Subject(s)
Basilar Artery , Cost-Benefit Analysis , Thrombectomy , Humans , Delivery of Health Care , East Asian People , Stents , Thrombectomy/instrumentation , Thrombectomy/methodsABSTRACT
Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.
Subject(s)
Proviruses , Viruses , Proviruses/genetics , Ecosystem , Oceans and Seas , Genome, Viral , Bacteria/genetics , Viruses/genetics , PhylogenyABSTRACT
Objective: To investigate the relationship between isocitrate dehydrogenase (IDH) 1/2 mutation, telomerase reverse transcriptase (TERT) gene promoter mutation and the prognosis of human glioma patients. Methods: One hundred fifteen patients with human glioma, treated surgically in The First Affiliated Hospital of Hebei North University from January 2019 to January 2020, were included. All patients were followed up until January 31, 2022. The mutations of IDH1/2 and TERT promoter were analyzed, and risk factors affecting survival of the patients with glioma were assessed. Results: IDH1 gene mutation occurred in 82 cases, IDH2 gene mutation occurred in five cases and TERT promoter mutation occurred in 54 cases. Univariate analysis showed that tumor WHO grade, resection range, preoperative Karnofsky performance status score, postoperative radiotherapy and chemotherapy, IDH1/2 gene and TERT promoter mutation influenced postoperative survival of patients with glioma (P<0.05). Kaplan-Meier survival curve showed that IDH1/2 gene and TERT promoter mutation were significantly different from those of wild-type patients (P<0.05). Conclusion: IDH1/2 gene and TERT promoter mutations are more frequent in patients with human glioma. These related factors can be used as molecular markers to aid in the prognosis of patients with glioma.
ABSTRACT
Endonuclease V (EndoV), which is widespread in bacteria, eukarya and Archaea, can cleave hypoxanthine (Hx)-containing DNA or RNA strand, and play an essential role in Hx repair. However, our understanding on archaeal EndoV's function remains incomplete. The model archaeon Sulfolobus islandicus REY15A encodes a putative EndoV protein (Sis-EndoV). Herein, we probed the biochemical characteristics of Sis-EndoV and dissected the roles of its seven conserved residues. Our biochemical data demonstrate that Sis-EndoV displays maximum cleavage efficiency at above 60 °C and at pH 7.0-9.0, and the enzyme activity is dependent on a divalent metal ion, among which Mg2+ is optimal. Importantly, we first measured the activation energy for cleaving Hx-containing ssDNA by Sis-EndoV to be 9.6 ± 0.8 kcal/mol by kinetic analyses, suggesting that chemical catalysis might be a rate-limiting step for catalysis. Mutational analyses show that residue D38 in Sis-EndoV is essential for catalysis, but has no role in DNA binding. Furthermore, we first revealed that residues Y41 and D189 in Sis-EndoV are involved in both DNA cleavage and DNA binding, but residues F77, H103, K156 and F161 are only responsible for DNA binding.
Subject(s)
Deoxyribonuclease (Pyrimidine Dimer) , Sulfolobus , Deoxyribonuclease (Pyrimidine Dimer)/chemistry , Deoxyribonuclease (Pyrimidine Dimer)/genetics , Deoxyribonuclease (Pyrimidine Dimer)/metabolism , Sulfolobus/genetics , Sulfolobus/metabolism , DNA Repair , DNA Damage , DNAABSTRACT
Uracil DNA glycosylase (UDG) can remove uracil from DNA, thus playing an essential role in maintaining genomic stability. Family IV UDG members are mostly widespread in hyperthermophilic Archaea and bacteria. In this work, we characterized the family IV UDG from the hyperthermophilic crenarchaeon Sulfolobus islandicus REY15A (Sis-UDGIV) biochemically, and dissected the roles of nine conserved residues in uracil excision by mutational analyses. Biochemical data demonstrate that Sis-UDGIV displays maximum efficiency for uracil excision at 50 °C ~ 70 °C and at pH 7.0-9.0. Additionally, the enzyme has displays a weak activity without a divalent metal ion, but maximum activity with Mg2+. Our mutational analyses show that residues E48 and F55 in Sis-UDGIV are essential for uracil removal, and residues E48, F55, R87, R92 and K146 are responsible for binding DNA. Importantly, we systemically revealed the roles of four conserved cysteine residues C14, C17, C86 and C102 in Sis-UDGIV that are required for being ligands of FeS cluster in maintaining the overall protein conformation and stability by circular dichroism analyses. Overall, our work has provided insights into biochemical function and DNA-binding specificity of archaeal family IV UDGs.
Subject(s)
Sulfolobus , Uracil-DNA Glycosidase , Uracil-DNA Glycosidase/chemistry , Sulfolobus/genetics , Amino Acid Sequence , DNA/metabolism , DNA Repair , Archaea/metabolism , Uracil/metabolismABSTRACT
USP7 emerges as a potential therapeutic target for cancers, as it plays an important role in the development of tumorigenesis by stabilizing multiple cancer-relevant proteins. Nevertheless, the discovery of drug-like USP7 inhibitors remains challenging. Herein, we report a series of N-benzylpiperidinol derivatives as potent and selective USP7 inhibitors (e.g., X20 and X26: IC50 = 7.6 and 8.2 nM), whose binding modes were revealed by crystallographic studies to be distinct from the known N-acylpiperidinol USP7 inhibitors. Among them, X36 with good oral PK profiles (rat: F = 40.8% and T1/2 = 3.5 h) exhibited significant antitumor efficacy in the MC38 colon cancer syngeneic mouse model, at least partly through upregulating the tumor infiltration of CD8+ T, NK, and NKT cells and downregulating that of Tregs and MDSCs. These findings may further pave the way for the development of USP7 inhibitors as novel cancer immunotherapy drugs.
Subject(s)
Colonic Neoplasms , Mice , Rats , Animals , Ubiquitin-Specific Peptidase 7 , Cell Line, Tumor , Colonic Neoplasms/drug therapyABSTRACT
Uracil DNA glycosylase (UDG) can excise uracil from DNA, thus playing an essential role in counteracting mutations. The genome of the hyperthermophilic crenarchaeon Sulfolobus islandicus REY15A encodes one putative Family V UDG (Sis-UDGV). Herein, we provide evidence that Sis-UDGV is a bi-functional glycosylase that can not only excise uracil from DNA, but cleave the generated apurinic/apyrimidinic (AP) site, which differs from other reported mono-functional Family V UDG homologs. Intriguingly, the enzyme can cleave DNA containing an AP site, thus suggesting that it might be involved in AP site repair. Biochemical data demonstrate that Sis-UDGV displays maximum activity for uracil removal at 45 °C â¼ 65 oC and at pH 8.0 â¼ 9.0. Furthermore, Sis-UDGV displays a substrate preference for uracil-containing ssDNA over uracil-containing dsDNA, but has no activity and weak activity for excising hypoxanthine from ssDNA and dsDNA, respectively. Importantly, we dissected the roles of seven conserved residues in Sis-UDGV by mutational analyses, demonstrating that residues D91, E117, E128, H167 and R192 are essential for catalysis. To our knowledge, it is the first report on the novel Family V UDG from Archaea with bi-functionality that harbors glycosylase/AP lyase activity.
Subject(s)
Sulfolobus , Uracil-DNA Glycosidase , Uracil-DNA Glycosidase/metabolism , Sulfolobus/genetics , Sulfolobus/metabolism , Uracil , DNA Repair , DNAABSTRACT
Apurinic/apyrimidic (AP) sites are severe DNA damages and strongly block DNA extension by major DNA polymerases. Y-family DNA polymerases possess a strong ability to bypass AP sites and continue the DNA synthesis reaction, which is called translesion synthesis (TLS) activity. To investigate the effect of the molecular structure of the AP site on the TLS efficiency of Dbh, a Y-family DNA polymerase from Sulfolobus acidocaldarius, a series of different AP site analogues (various spacers) are used to characterize the bypass efficiency. We find that not only the molecular structure and atomic composition but also the number and position of AP site analogues determine the TLS efficiency of Dbh. Increasing the spacer length decreases TLS activity. The TLS efficiency also decreases when more than one spacer exists on the DNA template. The position of the AP site analogues is also an important factor for TLS. When the spacer is opposite to the first incorporated dNTPs, the TLS efficiency is the lowest, suggesting that AP sites are largely harmful for the formation of hydrogen bonds. These results deepen our understanding of the TLS activity of Y-family DNA polymerases and provide a biochemical basis for elucidating the TLS mechanism in Sulfolobus acidocaldarius cells.
Subject(s)
Sulfolobus acidocaldarius , DNA/chemistry , DNA Damage , DNA Repair , DNA Replication , DNA-Directed DNA Polymerase/genetics , Sulfolobus acidocaldarius/genetics , Sulfolobus acidocaldarius/metabolismABSTRACT
Glioblastoma (GBM), which occasionally occurs in pediatric patients, is the most common tumor of the central nervous system in adults. Clinically, GBM is classified as low-grade to high-grade (from 1 to 4) and is characterized by late discovery, limited effective treatment methods, and poor efficacy. With the development of immunotherapy technology, effective GBM treatment strategies are of great significance. The main immune cells found in the GBM tumor microenvironment are macrophages and microglia (MG). Both these monocytes play important roles in the occurrence and development of GBM. Macrophages are recruited during tumorigenesis, whereas MG is present in the brain during embryonic development. Interestingly, the accumulation of these monocytes is inversely proportional to the survival of adult GBM patients but not the pediatric GBM patients. This study used single-cell RNA-seq data to reveal the heterogeneity of MG in tumor lesions and to explore the role of different MG subtypes in the occurrence and development of GBM. The results may help find new targets for immunotherapy of GBM.
Subject(s)
Brain Neoplasms , Glioblastoma , Adult , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Child , Gene Expression Profiling , Glioblastoma/pathology , Humans , Macrophages , Microglia/pathology , Tumor Microenvironment/geneticsABSTRACT
Dissolved organic matter (DOM) is an active component of organic manure that is widely used in agroecosystems to increase nutrient availability and consequently enhance crop yields. However, the ways in which soil DOM characteristics are influenced by organic manure and how it contributes to crop yield and soil P availability remains unclear. Here, we conducted a 5-year field experiment and demonstrated that partial replacement of chemical P fertilizer with swine manure could maintain high rice yield and soil available P levels and increase P fertilizer use efficiency (PUE) in comparison to chemical fertilization, even when the total P input was reduced. This suggests that organic manure application can significantly mobilize soil P and increase P availability. Structural equation modeling analysis indicated that the soil pH and humification degree of DOM, rather than DOM content, directly decreased maximum P adsorption capacity. The combined results of the optical spectroscopy and ultrahigh-resolution mass spectroscopy obtained from the laboratory validation experiment based on the DOM-removed soil demonstrated that manure-derived DOM competing with P for adsorption was one of the main reasons for the increase in soil P availability and that the effective DOM components were N-containing lignins, tannins, and condensed polycyclic aromatics with higher O/C and lower H/C ratios. Overall, our results provide solid evidence that soil DOM characteristics are influenced by manure application and facilitate soil P availability, which could help guide the sustainable P management and manure application in agroecosystems.